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Bug 596302 - dev-libs/xapian-1.2.24 sandbox violation
Summary: dev-libs/xapian-1.2.24 sandbox violation
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal with 1 vote (vote)
Assignee: Anthony Basile
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2016-10-06 05:31 UTC by ta2002
Modified: 2017-04-13 23:03 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build log (file_596302.txt,11.64 KB, text/plain)
2016-10-06 05:31 UTC, ta2002
Details
build log (1.2.24) (20161231-071031.log,11.49 KB, application/octet-stream)
2016-12-31 07:20 UTC, ta2002
Details
build log (1.2.24) (20161231-071031.log,11.49 KB, text/plain)
2016-12-31 07:22 UTC, ta2002
Details

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Description ta2002 2016-10-06 05:31:09 UTC
Created attachment 449296 [details]
build log

Don't know what is going on here, but surely ebuilds are not supposed to be trying to remove things in /usr/local.

Encountered this as a result of updating kde (including khelpcenter, which now requires xapian :( ).

Will attach build log.

# emerge -p --info
Portage 2.3.0 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.22-r4, 4.4.21-gentoo x86_64)
=================================================================
System uname: Linux-4.4.21-gentoo-x86_64-Intel-R-_Core-TM-_i5_CPU_750_@_2.67GHz-with-gentoo-2.2
KiB Mem:    12302196 total,   2714476 free
KiB Swap:    4112604 total,   4112604 free
Timestamp of repository gentoo: Tue, 04 Oct 2016 03:00:01 +0000
sh bash 4.2_p53
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.2_p53::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.22.2::gentoo
dev-lang/python:          2.7.10-r1::gentoo, 3.4.3-r1::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r1::gentoo
sys-devel/autoconf:       2.69::gentoo
sys-devel/automake:       1.12.6::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r4::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="64bit R X a52 aac aalib accessibility acoustid acpi additions adobe-cff aio alsa amd64 ap arcade asf aspell audio audiofile avcodec avformat blksha1 bluray bookmarks bwscheduler bzip2 cacert cairo caps cdda cdio cdr chm chroot cli client consolekit cpumining cracklib crypt cryptsetup css cups cxx dbus device-mapper dga directfb display-manager djvu downloadorder dri dri3 dvbpsi dvd dvdnav dvdr ebook egl eigen encode espeak exceptions exif expat fam fbcon ffmpeg filecaps flac fluidsynth fontconfig fortran gallium gbm gcj gcrypt ggi gif glamor glib glibc-omitfp gmp gpg gphoto2 gpm gsm gstreamer gtk handbook hardcoded-tables hddtemp hpn iconv idea imap infowidget inotify iostats ipc ipfilter ipv6 jabber jbig jit joystick jpeg jsbsim kdcraw kde kmod kscreen lame lcms less libass libkms libmpv libsamplerate libwww live lm_sensors logviewer lzma mad matroska mbox mdns-bundled memlimit midi minizip mmx mmxext mp3 mp4 mpeg mta mudflap multilib nas ncurses net network nls no-old-linux nodrm npm nptl ntfsprogs ntp ocamlopt offlinehelp ofx ogg okular opengl openmedia openmp opus oscar osdmenu p2p pcre pdf pie pm-utils png policykit portmon postproc ps qml qt3support quotes raptor readline real recursion-limit redland rtc rtmp savedconfig scanfolder scanner scrypt sdl search seccomp secure-delete sensord shared-glapi shm silc smbclient smtp snapshot sndfile sound speex spell sse sse2 sse2_4way sse2check sse4 ssl ssse3 stats subversion svg swscale sysfs taglib tcmalloc tcpd theora threads threadsafe tiff tls-heartbeat truetype udev udisks unicode upower urandom usb userlocales utils v4l2 vdpau video vorbis vtv wav webdav-neon webinterface widgets x264 xcb xinerama xml xmp xpdf-headers xslt xv xvid yahoo zlib zrtp" ABI_X86="64" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="author braindump flow karbon krita sheets stage words" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext popcnt sse sse2 sse3 ssse3 sse4_1 sse4_2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev" KERNEL="linux" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Anthony Basile gentoo-dev 2016-10-07 17:23:25 UTC
(In reply to ta2002 from comment #0)
> Created attachment 449296 [details]
> build log
> 
> Don't know what is going on here, but surely ebuilds are not supposed to be
> trying to remove things in /usr/local.
> 
> Encountered this as a result of updating kde (including khelpcenter, which
> now requires xapian :( ).

I have no idea either.  I'm not hitting it and neither did the arch testers, so something change wrt to kde update.  Can you try 1.2.24 and see if that makes a difference.  I may have to set up a kde system.
Comment 2 ta2002 2016-10-08 17:50:00 UTC
> Can you try 1.2.24 and see if that makes a difference.
> I may have to set up a kde system.

Behaved exactly the same.

I was able to install the package by (temporarily) doing:

chmod 000 /usr/local/lib64/

but that doesn't really explain why this is happening. Also, that caused a different package (sys-apps/accountsservice) to crash, but by that point, xapian was installed, so I just changed the permissions back to 755, and resumed.

The only thing I have in there is a program to manipulate virtual machine disk images (vmware-vdiskmanager, which I found on the vmware web site).
Comment 3 ta2002 2016-12-31 07:20:08 UTC
Created attachment 458080 [details]
build log (1.2.24)

Problem is still there as I am trying to update KDE again.
Comment 4 ta2002 2016-12-31 07:22:32 UTC
Created attachment 458082 [details]
build log (1.2.24)

Upload attachment as the content auto-detector can't seem to recognize plain text.
Comment 5 Anthony Basile gentoo-dev 2016-12-31 11:17:58 UTC
(In reply to ta2002 from comment #4)
> Created attachment 458082 [details]
> build log (1.2.24)
> 
> Upload attachment as the content auto-detector can't seem to recognize plain
> text.

Here's what I'm thinking: libvixDiskLib.so.5 is a vmware library that lives under /usr/local.  The sandbox violation appears to happen right after configure phase when ldconfig is run.  With the -N flag, sym links are updated.  ldconfig tries to update sym links in /usr/local so sandbox throws a violation.

Can you investigate along these lines.  I don't think this is a problem in xapian or its ebuild.
Comment 6 ta2002 2017-04-13 23:03:40 UTC
You are probably right about the cause, but why is xapian the only package I have ever seen (in almost fifteen years running Gentoo) to have this problem?